Plant Molecular Biology

, Volume 85, Issue 4–5, pp 485–503 | Cite as

Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing

  • Hifzur Rahman
  • N. Jagadeeshselvam
  • R. Valarmathi
  • B. Sachin
  • R. Sasikala
  • N. Senthil
  • D. Sudhakar
  • S. Robin
  • Raveendran Muthurajan


Finger millet (Eleusine coracana L.) is a hardy cereal known for its superior level of tolerance against drought, salinity, diseases and its nutritional properties. In this study, attempts were made to unravel the physiological and molecular basis of salinity tolerance in two contrasting finger millet genotypes viz., CO 12 and Trichy 1. Physiological studies revealed that the tolerant genotype Trichy 1 had lower Na+ to K+ ratio in leaves and shoots, higher growth rate (osmotic tolerance) and ability to accumulate higher amount of total soluble sugar in leaves under salinity stress. We sequenced the salinity responsive leaf transcriptome of contrasting finger millet genotypes using IonProton platform and generated 27.91 million reads. Mapping and annotation of finger millet transcripts against rice gene models led to the identification of salinity responsive genes and genotype specific responses. Several functional groups of genes like transporters, transcription factors, genes involved in cell signaling, osmotic homeostasis and biosynthesis of compatible solutes were found to be highly up-regulated in the tolerant Trichy 1. Salinity stress inhibited photosynthetic capacity and photosynthesis related genes in the susceptible genotype CO 12. Several genes involved in cell growth and differentiation were found to be up-regulated in both the genotypes but more specifically in tolerant genotype. Genes involved in flavonoid biosynthesis were found to be down-regulated specifically in the salinity tolerant Trichy 1. This study provides a genome-wide transcriptional analysis of two finger millet genotypes differing in their level of salinity tolerance during a gradually progressing salinity stress under greenhouse conditions.


Eleusine coracana Salinity response Transcriptome analysis RNA-sequencing Pathway mapping 



The financial support of Department of Biotechnology, Government of India, New Delhi (Grant Number BT/PR-10482/AGR/02/564/2008) is greatly acknowledged. The authors are also grateful to CLC Genomics Workbench support team for their help in analyzing the transcriptome data.

Supplementary material

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Supplementary material 1 (DOCX 1459 kb)


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© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Hifzur Rahman
    • 1
  • N. Jagadeeshselvam
    • 1
  • R. Valarmathi
    • 1
  • B. Sachin
    • 1
  • R. Sasikala
    • 1
  • N. Senthil
    • 2
  • D. Sudhakar
    • 1
  • S. Robin
    • 3
  • Raveendran Muthurajan
    • 1
  1. 1.Department of Plant Biotechnology, Centre for Plant Molecular Biology and BiotechnologyTamil Nadu Agricultural UniversityCoimbatoreIndia
  2. 2.Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and BiotechnologyTamil Nadu Agricultural UniversityCoimbatoreIndia
  3. 3.Department of Rice, Centre for Plant Breeding and GeneticsTamil Nadu Agricultural UniversityCoimbatoreIndia

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